NMR solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N⁴-etheno-2'-deoxycytidine opposite thymidine: Comparison with the duplex containing deoxyadenosine opposite the adduct

The exocyclic 3,N⁴-etheno-2'-deoxycytidine adduct was incorporated at the center of the oligodeoxynucleotide duplex d(C-G-T-A-C-εC-C-A-T-G-C)- d(G-C-A-T-G-T-G-T-A-C-G), and its solution structure was analyzed using high- resolution proton NMR spectroscopy and molecular dynamics simulations. The experimental data indicate that the oligodeoxynucleotide duplex adopts a right-handed helical structure with sugar puckers in the C2'-endo/C3'-exo range and Watson-Crick hydrogen bond alignments for all base pairs. NOE connectivities established a syn orientation for the glycosidic torsion angle of the exocyclic adduct. Restrained molecular dynamics simulations, using the full relaxation matrix approach, produced a three-dimensional model in agreement with the experimental data. The structure shows only minor perturbations in the sugar-phosphate backbone and a 27° bend of the helical axis at the lesion site. On the refined model a well-formed hydrogen bond between T(N3H) and εC(N4) stabilizes the εC(syn)-T(anti) base pair alignment, reflecting the preference of the adduct for the syn orientation. Furthermore, the εC(syn)-T(anti) base pair stacks with flanking base pairs. We discuss a correlation between the mutagenic properties of the adduct and the three-dimensional structure of the εC-dA and εC-T duplexes.